Not Alone: The Atlantis Continuum
by Storyteller09
Summary: Who honestly believes that SG-1 was the only ones in a wormhole while time rewrote itself? 'Cause this time... they're not. Pairings will be eventually Shweir, Sam/Jack, McKeller, sort of Ronon/Teyla. Set during Continuum and after 'The Seed'.
1. Chapter 1

A/N: I'm sorry... really, I am. I know I have other stories I should work on... a lot of them. But... I wants feedback on this idea. I have about 8 pages written in Word and I really can't stop thinking about this idea. And it's horrible because this preview is so short and I have Fixing Destiny and Sang Real to work on (and like three other AUs that have popped onto my hard drive mysteriously... *looks at fingers in betrayed horror*). I think I need a beta. Really, guys, I need someone who will read my WIP and point me in the right direction and give me ideas and not let me abandon my stories for six months. Anyone? Ok, onto the actual story: Spoilers for Stargate: Continuum and at least a rudimentary knowledge of SGA going ons up to 'The Seed.'

Not Alone: Atlantis Continuum

"Go." General O'Neill gasped out his final words, ordering them through the gate. Colonel Carter stared in shock as her closest friend (and recently more than that) for the last ten years died in her arms. Mitchell pulled her up and shoved her towards the gate.

Meanwhile, in the Pegasus galaxy…

"Are you sure you got everything, Rodney?" Lieutenant Colonel John Sheppard teased the wayward scientist as he rushed up. The man glared at him indignantly.

"I believe so." He answered snidely. Sheppard smirked.

"I don't get why you had to bring along so much stuff anyway; it was just a ceremony for Torren, not a weeklong trip to Wraith-infested territory. I mean, really, two laptops?" Sheppard raised his eyebrows. "And all this Ancient interface stuff? What exactly have you been up to these last two days?"

"Well pardon me for not wanting to stop on this project I've been working on for the last three months." He harrumphed and rolled his eyes. "I've been trying to create an interface program that even your most boneheaded grunts could use."

"Does this mean you don't count me in that group? Rodney, I'm touched." Sheppard grinned good-naturedly as he waved his hand in dismissal. The guy really had come a long way. Their conversation was interrupted by the rest of their group arriving. Ronon, Dr. Keller, and Teyla, with Torren tucked into a carrying sling, all walked into the clearing carrying their bags. "Where's Kanaan?"

"He will be following shortly. His family wished to speak with him as he has decided to return to Atlantis with Torren and myself. I do not want to intrude, not when he is sacrificing his ties to the others by living in Atlantis and not on New Athos." Teyla adjusted Torren carefully, not wanting to wake him. They had spent the last two days on New Athos, settling in the recently rescued Athosians and finally celebrating the Torren's birth with an Athosian version of a christening. Keller was here to a) keep an eye on John who had insisted on coming despite the fact he was still recovering from having the Wraith hive tendril stabbed into his still tender side and b) to finish her checkups on the Athosians. The fact that it was Torren's first gate trip made everyone a little nervous (despite knowing that many Pegasus natives had carried their newborns through the Stargate for millennia) and Keller's presence had reassured the new mother and her (slightly) overprotective teammates.

"All right dial it up, Rodney." Sheppard ordered, McKay moving before he'd even finished speaking. Yes, the Pegasus galaxy had done wonders for his disposition. Their IDC was sent and they stepped forward into the gate, eager to return to Atlantis. Sheppard and Ronon, always wary, lagged a half-step behind and were the only ones to see the slight blurring as reality seemed to shift. Before they could react, their momentum carried them into the wormhole.

***

"Oh..." Rodney's voice trailed off, doubtlessly ending in some profanity too harsh for Torren to learn just quite yet. Instead of being greeted with a brightly lit gate room with Woolsey looming over them to welcome them back, Atlantis was dark. It was pitch black as they stepped in, only brightening as the two with the gene made their way into the center of the room.

"What?" Sheppard looked around and immediately assumes the worst. "Damn it, Rodney, not again!"

***

A/N: My A/Ns are longer than the story... crap. So please, someone needs to ride herd on me and make sure I work (besides college work that is probably slightly higher on my priorities... at least it should be) on this stuff. Please give me honest feedback! And no FLAMES! I got a sorta almost one on Fixing Destiny and I haven't been able to write anything for the last two months out of pure self-doubt.


	2. Chapter 2

A/N: No reviews... at all. I'm a bit disappointed... Though there was a story alert and a story fav, so at least some people are enjoying this. I know the chaps are really short, but I don't want to give away too much at once... anywhere here's the next tidbit.

***

"It wasn't me, Sheppard, I swear! We haven't touched the gate program since after you got back. Everything was fixed!" Rodney responded defensively.

"I swear to God, if I'm 48,000 years in the future again, I'm going to throw you into the ocean… or more likely sand seeing as the ocean had dried up by then." Sheppard threatened. Rodney grabbed his laptops and headed up to the control room to see just what the heck was going on. Sheppard, however, looked up at the window, frowning. His eyes widened. "Rodney! We're underwater!"

"What, again?" Rodney typed something in and frowned. "This doesn't make any sense… it says we're on the original Lantea, not M35-117. And Atlantis's internal clock of sorts is reading as if it was the day we left New Athos, but none of these systems register being activated in over ten millennia. It's like the expedition never existed!"

"Wait a second… right before I stepped into the wormhole, I thought I saw this tree blur, kind of like reality distorting. Could some kind of weapon have done this? Made it where we never existed?" Sheppard theorized blindly, not sure if what he was suggesting was even possible. Rodney thought a second and snapped his fingers.

"The temporal studies lab!" He exclaimed. The others raised their eyebrows and waited for him to explain. H e walked off in the direction of the labs, but suddenly came running back. He immediately started typing commands into the laptop, fingers flying frantically. He seemed to finish and leaned back. "Brace yourselves."

"What'd you do?" Sheppard asked, worried.

"Every second we sit on the ocean floor we sit on the ocean floor drains power from the ZedPM. I'm raising the city." Rodney grabbed onto a nearby console as the rumbling began, the others quickly following suit. Ronon grabbed Teyla, holding her securely so Torren wouldn't bump into anything. She nodded her thanks after the rumbling stopped and Atlantis surfaced. Sheppard grimaced. As bad as not knowing what was going on was (and being on the ocean floor with very limited power), he didn't like being out on the open ocean, an easy target.

"Can we cloak?" He asked uneasily. Rodney considered the request carefully.

"I suppose the emitters are still the same… and I think I still remember how we wrote the program. I think so. Give me an hour. Meanwhile, I need you to run down to the chair room and run a full diagnostic. I need to know everything that's going on with the city to figure out just where we are. And you'll be available for shooting anybody who comes sniffing around." Rodney turned to the deep space sensors and activated them. The screen seemed clear… too clear. The _Daedalus_ had been a few days out when they had left for New Athos; by now it should have almost been to the city. Of course they did seem to be on a different planet now, but its disappearance was unsettling. Keller made her way to the infirmary to see what supplies she could scrounge up, while Teyla and Ronon looked on with worry. What the heck had happened here?

***

A/N:Yes, they are on a different planet; I figure that if the Stargate were to move while they were in transit that the wormhole would follow. That's why SG-1 ended up in Antarctica and not underneath Cheyenne mountain.


	3. Chapter 3

A/N: Ok, still a short chapter, but at least the muse is still flowing.

***

It took them three months to get to Earth. After the initial 'oh, crap, someone f-ed with the timeline, we should go fix it' and figuring out the epicenter of the time distortion (as Rodney deemed it) lay in the Milky Way, they decided that the only way they were going to figure out the whole story was to see what detail had changed in Earth's history. Sheppard actually had the bright idea of the Dagan world's ZPM as a power source. The mission to retrieve it took the better part of a week even though they already knew where all the pieces were (there were only four of them to dig; Keller had taken to babysitting both Torren and Atlantis). The mood had been somber afterwards though; sometime in the last four years the Dagans had been culled. Completely. Alina and the other members of the Order hadn't located the ZPM without Atlantis's help so it was still buried safely away underground, but the absolute lack of people was depressing. The second city ship secretly provided another partially charged ZPM (at least this way the Lord Protector couldn't keep up the royal act and the people had a chance at revolution, though the team didn't stick around to help) and as many drones as they could fit into the two jumpers. Various other planets provided food and, in one case, a second charged ZPM. Finally, they were ready to make the journey to Earth. The trip back to the Milky Way was a nerve-wracking one, wondering what was happening back on Earth and if they would be able to fix it. Rodney (in one of his admittedly smarter moments) managed to get the shield and cloak programs to actually cooperate, which meant that they wouldn't be noticed in orbit around Earth by the actual deep space telemetry technicians. Sheppard slid them easily into high orbit (to hopefully avoid knocking any satellites out of the air) and they peered down at the small blue and green world.

"Now what?" Sheppard asked as Teyla and Ronon were greeted with the Earthling's homeworld in all its splendor. Rodney bit his lip, uncertain.

"First things first, I guess. I'll tap into one of the satellites and piggy back a signal to get to their database and see what's going on." He tried to sound confident, but truthfully he wasn't sure how the time distortion had happened in the first place, much less how to fix it. A sudden ping from one of the sensors had their heads turning. Two more followed it. Three dots appeared on the readout, all located in the U.S. "Transmitter beacons?!"

"You mean there's an SGC down there?" Sheppard asked, hopeful. Rodney considered the locations and shook his head.

"There are only the three beacons and they're registering on our code system." He announced proudly.

"You mean other people managed to make it through the time distortion intact as well?" Dr. Keller had long since learned that she might as well stay up in the control room, the eerily empty infirmary was just too much for her to handle.

"Not just anyone!" Rodney actually sounded excited. "It's SG-1!"

***

A/N: Yay! Atlantis to the rescue!


	4. Chapter 4

A/N: This first scene is exactly what inspired this story when I watched Continuum and the whole separation thing was put into place. For people who were practically family, it must have been hell to be all alone in a world where everything you know may be wrong.

***

They picked up Sam first, mainly because she stood as their best bet for figuring out what comes next. They were all pretty pissed about the restrictions that were listed on her file. This was one of the first people to step through the gate and a former leader of Atlantis. And now she was being monitored constantly and cut off from any and all of her former friends. Her reaction to Sheppard's arrival was easily understandable after reading the reports the people in authority had filed. Sheppard lurked around her house until she came home, calling out to as she got out of the car. "What's up, Colonel?"

"I'm sorry you must have me confused with someone else…" Her subdued dismissal trailed off as she recognized his voice. She whirled, dropping several papers in her haste. When she spoke her voice was disbelief, confusion, and a heartbreaking amount of relief. "Sheppard?!"

"Yep." He answered, grinning. Finding out that she was still… herself… had been just the morale booster the team had needed. He froze as she left the car door standing wide open and wrapped her arms around him. He swore he could feel her crying as she crushed him to her in an attempt to assure herself that she was no longer alone. He held her as best he could without feeling too awkward, knowing from the report what had happened and that she needed someone to hold her. From what he could tell from the reports, General O'Neill had died in her arms. "You're gonna be okay, Sam. We're here to help."

"Thank God." She whispered fervently, withdrawing slightly and wiping at stubborn tears. She looked up at him and noted his Atlantis patch on his uniform. "How?"

"The strangest thing happened on our way back from Torren's christening thing-y…" He started to explain, but (as usual) Sam was way ahead of him.

"You were in the wormhole when it hit, just like we were." She said, realization dawning.

"We ended up in Atlantis at the bottom of the ocean. McKay managed figure out enough to know that should probably get back here as soon as possible. We managed to gather enough food for us to live on, Ronon started hunting deer and game for us, and we scrounged up enough ZPM power to get here." He nodded. They gathered up her stuff and headed inside so they could finish their conversation in private. He explained what they had been up to for the last few months and she started cooking and packing. As useless as she'd been, she desperately needed to do something to help so she cooked up a veritable banquet of food that they could take back to the others. "We found your transmitters still broadcasting away and figured it was about time something went right. I've got a jumper waiting right outside and we can leave whenever you're ready."

"So Atlantis is really here? In orbit?" She asked, relieved beyond words. He nodded and told her about the modifications to the shield cloak. Her eyes lit up at the mention of the technology and he had to wince at the fact that she'd been here all this time with no way to actually work or help anyone. He made himself useful by wrapping up the food in dishes while she cleaned up. "We should probably stop by and get at least one more laptop. I have one and the others should have some too, but we're going to need all the computing power we can get our hands on. I can't believe I'm this excited to go to Radio Shack."

"Well, we've got the deep space sensors on full power, so we should have ample warning of any of Ba'al's movements. We're safe for now." He reassured her. A sudden quiet tapping on the door made them tense and stop in their tracks. Sam's eyes widened.

"Oh, crap… I forgot I'd invited her." She looked at Sheppard almost apologetically as she went to open the door. Her greeting to the woman she let inside made Sheppard's heart freeze. He looked over at the oh-so-familiar green eyes and short black hair and his brain came to a shuddering halt. He finally managed to spit out a word, the only word that mattered. "Elizabeth."

***

A/N: I warned you it would eventually be Shweir... don't act so surprised. YAY for my first review!!!!! It made my day.


	5. Chapter 5

A/N: Yay for reviews! Not that I'm holding you guys hostage (I'm really not, I swear), but it is so much easier to write when I'm motivated by nice words. So late, yes, but thankfully moving. Hopefully I'll keep unblocked. :D

Chapter Five

***

"_Elizabeth."_

"Oh, have we met?" Her eyes didn't light up in recognition and her voice, while warm, was that of a stranger meeting someone new. He gulped and looked to Sam for guidance.

"I…" Sam started to make an excuse, but stopped. She seemed to decide something important and shook her head. "You know what? No more. No more lies and half-truths. I'm sick of being Professor Tapping at University of Washington. John… I can't lie to her anymore. I couldn't believe my eyes when I started teaching freshman math at the college, but it was actually her. She's the Dean of the Political Science department."

"What's going on here?" Weir was confused and clung to her coat like a lifeline. "Who is this, Amanda?"

"My name is Lieutenant Colonel John Sheppard of the U.S. Air Force and that is not Amanda. Her name is Colonel Samantha Carter." He answered, still staring at her. She seemed to back up, obviously unnerved by the revelation.

"Like the astronaut?" She finally asked Sam.

"I'm not an astronaut. At least… not in my timeline." Sam shook her head. Weir raised her eyebrows but didn't back down again. "John… we're never going to convince her."

"Yeah, we will. Grab the food. And we're kind of short on cash, as in bankrupt, since we don't usually carry any… um, where we are. Oh, and Rodney demands coffee. Demands it." He added with a smirk. They'd all been suffering caffeine withdrawal the past few months. They left Elizabeth seated in the living room and gathered up anything and everything they thought they might need. She ended up taking all of her clothes (if she didn't use them, Keller and Teyla could), her laptop, and several other bags of stuff. It was clear that she was severing all ties with this false life. Once they had the cloaked jumper loaded, they came back in. "Thanks for waiting, Elizabeth."

"I take it you're going somewhere, 'Sam'?" Elizabeth asked. The two SG personnel traded looks.

"Actually, we're hoping you'll want to tag along." Sam finally broached the subject. "I know this is going to sound hard to believe, but you have to trust us."

"What are you talking about?" She was looking at them like they'd lost their minds (John should know, he and Rodney had gotten that same exact look at least twice a week while she was still the expedition head). John didn't bother trying to explain it here; he just grabbed her hand and pulled her out the back door. Her hand tightened around his as he apparently vanished, but he just tugged her into the jumper. She gasped as she passed the cloak's field and stared in amazement at the alien technology inside. Once they'd convinced her to at least accompany them to Atlantis, they sat and filled her in one the story that was their lives. She sat back and watched as Sheppard easily maneuvered the small ship into the jumper bay of the city, her mind spinning. "This place is beautiful! Unbelievable… but beautiful."

"Well, it's been the Atlantis expedition's home for years. An expedition that, in our timeline, you led for three years." John told her, his voice low and subdued. At her startled look he told her about her capture and presumed death. "We're sorry to drag you into this, it's just been a while … and I couldn't leave you behind again. When we land the others might stare, but please don't be mad at us. You were the best leader Atlantis could have. No offense, Sam."

"None taken, Sheppard. In fact, I'd have to agree with you. Elizabeth Weir, in our timeline, was a great leader and a wonderful friend." Sam, though she had only known Weir for her short stint as the head of the SGC and the rare visits back to Earth, had seen the impact her death had on the expedition.

"So… in your timeline I get to live here. From what you've told me of the city, I'm pretty sure that I'd give anything to experience it." Dr. Weir said confidently. They made their way out of the jumper, Weir drinking in the strange beauty of the alien city. "I'm really glad you let me come along... and I'm glad I decided to come."

"Well, if it helps, I'm glad you trusted us enough to come, too." Sheppard answered awkwardly. Introductions were tense at first as everyone reacted to the presence of their long missing friend. Ronon's hands clenched as he stopped his standard reaction of drawing his gun when surprised (everyone still feared a repeat of the surprise birthday celebration fiasco even though it had been a couple of years). Teyla's reaction was merely wide eyes, but was accompanied by a gasp from Keller and a shockingly **speechless** Rodney McKay. Dr. Weir cleared her throat in embarrassment and everyone suddenly realized they were staring.

"Hi, my name is…" She started to feebly break the awkward silence, but was cut off by a recovering Rodney.

"Yes, yes, we all know who you are, Elizabeth. We're just… stunned by your arrival." McKay interrupted. "So, um, us! Right, we know you, you don't know us… so… hi. I'm Dr. Rodney McKay, multiple PhDs, Chief Science Officer of the Atlantis Expedition. The behemoth is Ronon Dex, Satedan/resident caveman/Wraith killer, the willowy brunette is Teyla Emmagen, leader of the Athosians and kickass fighter/negotiator, and the young blonde is Dr. Jennifer Keller, Chief Medical Officer of Atlantis. That is we were. In this timeline we're mostly dead or culled or… _worse_."

"Worse?" Elizabeth echoed faintly, slightly disturbed. John had to chuckle at her expression.

"Don't mind Rodney. He's just sore that he's an apparently very famous pianist in this timeline instead of a ground-breaking physicist." John explained. "He takes such things personally."

***

A/N: Poor Rodney. No coffee and he's a famous pianist in this timeline. Will horrors never cease? (Also... beta search is still open).


	6. Chapter 6

Chapter 6

"_He takes such things personally."_

"I see." She let out a small smile at the joke, but was still busy taking in the Ancient architecture that surrounded them. Sam took the chance to hug Keller and Teyla, shake hands with Rodney, and then got a slap on the back from Ronon (even his friendly moves left people with bruises). She grinned broadly at the Satedan's form of affection.

"Okay, we'll need to pick up Cam and Daniel quickly before the Air Force figures out where I vanished off to and get them whisked off to some bunker somewhere. They probably wouldn't be able to hide from us, but I'd rather not have to stun our way into our own people's base." Sam announced, ready to see her teammates again. Three months was a long forced absence and everyone was inwardly cringing at the fact that it could have been a lot longer if Atlantis hadn't shown up. "Luckily, the timelines are fractured off enough that entropic cascade failure won't occur for any of you. Daniel's still alive in this universe, so that's proof that you weren't all just protected by Atlantis. Now I've got a laptop, a coffeemaker, some grounded coffee beans, and a pissed off attitude. Rodney and I should be able to hack anything on this planet that has any semblance of connectivity." Sam looked grim at the statement, but had to smile at Rodney's near euphoric excitement at the words coffeemaker and coffee. "Sheppard, you better take Teyla with you when you pick Cam up. But you might want to let her change into some of the clothes I brought first. You'll have to pick up civvies from Cam. It's not a good idea to walk around with Atlantis uniforms on. Granted, most will think you're from a sci-fi convention, but word only has to reach those in authority and they'll know something's going on that shouldn't be. And then there's the fact that, while I can create a jamming device that knocked out the bugs in my house with spare parts from a cell phone and the clock radio, I highly doubt Col. Mitchell or Daniel can."

"A cell phone and a clock radio? Really?" John couldn't help but be doubtful. She shrugged lightly.

"I once met a guy who made a Stargate out of a lot of toasters and some platinum. Of course, he **was** an Ancient. Still, Rodney and I can rig up something portable to prevent any curious ears from listening in." She explained.

"You think a jamming device is neat? I built a nuclear bomb in sixth grade. All it lacked was fissionable material." Rodney's voice sounded wistful. Elizabeth stared at him in amazement.

"Forgive me, but you people are… odd." She crossed her arms and tried to look stern at the thought of sixth graders building nukes.

"Hell, we're just getting started." John let out a beaming grin.

"So you know that neighbor of yours is totally crushing on you, right?" John ghosted up to the car in his plain BDU shirt and pants with a small bag on his shoulder and took up a lazy sprawl against the doors. Cam, busy at work underneath the hood, nearly gave himself a concussion as he tried to pick his head up. His mouth opened and closed, but no sound came out. John continued on, cutting him off. "I'm just passing through, but I'd really like to meet some new people, so I thought, hey, guy working on car, go say hi. Maybe we could get together and have a beer, watch some football?"

"Wha…" Mitchell's face was comical in his confused state. Sheppard let his eyes dart around, signaling that it wasn't safe to talk outside. Mitchell's eyes widened and he continued as if he'd never met John before. "Well, I'm always up for some good company. Name's Cameron, but most people call me Cam."

"Nice to meet you, Cam. I'm John." Sheppard answered with a smirk. The two shook hands. "I really do hate to drag you away from this beauty."

"Nonsense. She'll be here later. Come on in and I'll get you a cold one." Mitchell led Sheppard inside. As soon as the front door shut, he whirled. Before he could say a word, Sheppard raised a hand and put a finger to his lips. John dug around a few seconds in his backpack and brought out a small electronic-looking device. With a simple flick of the switch, he nodded. "Thank God! I thought for a minute there you were this timeline's Sheppard. What's going on?"

"Sorry about the surprise. We've already picked up Col. Carter and the government's wavering about whether or not you and Daniel had something to do with it. You're being watched pretty closely and your house is bugged, so I had Teyla wait in the jumper and decided to come in as a random stranger." Sheppard explained.

"Jumper?!" Mitchell latched onto the word. John nodded and outlined what had happened in Pegasus. By the time he was done, Mitchell was beaming. "Now that's what I'm talking about!"

A/N: Well, not too shabby considering that finals start tomorrow. It feels good to write this universe. Helps me get my mind off of calculus (though my mind probably ought to be on the calculus anyway). Hope you enjoy!


End file.
